#!/bin/bash 
#
#  This script was supplied by Lisa M. Perez at the Laboratory
#     for Molecular Simulation at Texas A&M University and is provided
#     on an "as is" basis.
#
#     http://www.chem.tamu.edu/LMS
#
#  This script was specifically designed for use on hydra ( IBM p575 Cluster running LoadLeveler )
#
#  Revision: 01252008
#  Format: MMDDYYYY
#
#  04052007 added -y flag and changed walltime default from 1 hour to 24 hours
#  07022007 minor bug fix: quotes on Trap line caused errors
#  11082007 consumablmemory  changed to  ConsumableMemory
#  01252008 fixed example
#  02292008 changed parallel to serial for gaussian jobs since the parallel keyword is only for mpi jobs
#		and removed extra accounting summary at the end since it was also processed by the trap command
#  12272008 changed default g03 to revision D.02 in /usr/local/lms/g03_D02_new and need to set LIBPATH to point to older compiler
#
# ....................................................................        
rev=12272008
#  help function
gethelp ()
{
#clear
echo " "
echo " This script was specifically set up for the LoadLeveler queueing system on hydra.tamu.edu "
echo " and currently can submit G03 jobs to the smp_normal and smp_long queues"
echo " "
echo " Syntax : qprep [-n] [-l] [-32] [-64] [-128] [-256] [-n[x]] [-mb[y]] -gb[z] [-t[hh]] [-y] [-r] filename"
echo " "
echo " x     : number of processors requested and can have values that range from 1-592"
echo "       : non mpi jobs (ie. Gaussian) can have a range from 1-16"
echo "       : mpi jobs (ie. AMBER) can have a range from 16-592"
echo " "
echo " y     : memory requested in MB (ie. -mb500 would request 500MB)"
echo " z     : memory requested in GB (ie. -gb2 would request 2GB)"
echo " "
echo " Flags to specify the queue (requests the maximum walltime available)"
echo " smp_normal   smp_long     mpi32     mpi64    mpi128    mpi256"
echo "    -n           -l         -32       -64     -128       -256"
echo " "
echo " Alternatively, you may specify the walltime instead of using one of the queue flags"
echo " -t[hh] : hh is the number of walltime hours (ie. -t5 requests 5 hours of walltime)"
echo " "
echo " filename is the name of the input file (filename.com)"
echo " "
echo " The default program: g03, queue: smp_normal, memory: 8gb, processors: 8"
echo " "
echo "  NOTE : do NOT include %nproc or %mem in your input file (filename.com). The job file "
echo "         automatically sets the number of processors and the memory based on your flags."
echo " "
echo " If you wish to submit to the smp_long queue using 4 processors and 6gb of memory, "
echo " you will need to use the -l and -gb4 flags"
echo " "
echo "     example:  qprep -l -gb4 -n4 filename"
echo " "
echo "               The qprep -l -gb4 -n4 filename command will create filename.job and submit "
echo "               it to the smp_long queue with a request for 4gb of memory and 4 processors"
echo " "
echo "     example2: qprep -n -n12 -gb12 -t20 filename"
echo "               submits to the smp_normal queue and requests 12 processors, 12gb of memory, and 20 hours of walltime"
echo " "
echo " The -r flag is used to append the output to the output file instead of overwriting it." 
echo " The -y flag will not ask you to look over the job file and will automatically submit." 
echo " "
echo " USEFUL commands "
echo " "
echo " qlimit       lists queue names, their limits, and which queues have open slots"
echo " llclass      lists queue names and some of their limits"
echo " llclass -l   lists queue information in long format"
echo " llq          lists all jobs in the queueing system"
echo " llq -u user  lists the jobs jobs for user (user should be a username)"
echo " "
echo " man llq      manual pages for llq"
echo " man llclass"
echo " man llsubmit"
echo " "
echo " General step to submit a job to the queueing system"
echo " "
echo "  Step 1:  prepare your input file manually, using GaussView, Cerius, or "
echo "           your favorite interface"
echo "  Step 2:  use qlimit to determine which queue to submit to"
echo "  Step 3:  use qprep with the appropriate flags to create the job file and have it "
echo "           submitted to the appropriate queue"
echo " "
echo " To report problems with this script, e-mail Lisa M. Perez at mouse@mail.chem.tamu.edu"
echo " "
exit 0
}

# goto help if there are no arguments ................................
# ....................................................................        
if [ $# -eq 0 ]; then 
  gethelp
fi 

# ....................................................................        
# parameters .........................................................
# ....................................................................        
# mb - memory in MB -bg - memory in GB; t - walltime requested in hours
# t2 - queue name r - whether to overwrite output file
# or append to it; n - number of processors; p - program to use
# ttest - flag to see if -t was used

m=8gb
mg=1000000000
t=24
t2="smp_normal"
r=0
n=8
p=g03
ttest=0
ask=1

i=0
for flag in "$@"; do
  case "$flag" in 
      -h )
         gethelp
      ;;
      -help )
         gethelp
      ;;
      -mb[0-9]* )
         m=`echo $flag|sed 's/-mb//'`
         let "mg=$m*1000000/8"
         m=${m}mb
      ;;
       -gb[0-9]* )
         m=`echo $flag|sed 's/-gb//'`
         let "mg=$m*1000000000/8"
         m=${m}gb
      ;;
       -t[0-9]* )
         t=`echo $flag|sed 's/-t//'`
	 ttest=1
      ;;
       -n )
         if [[ $ttest -eq 0 ]]; then
           t=24
         fi
	 t2=smp_normal
      ;;
       -l )
         if [[ $ttest -eq 0 ]]; then
           t=96
         fi
         t2=smp_long
      ;;
       -32 )
         if [[ $ttest -eq 0 ]]; then
           t=24 
	 fi
         t2=mpi32
      ;;
       -64 )
         if [[ $ttest -eq 0 ]]; then
           t=12 
         fi
	 t2=mpi64
      ;;
       -128 )
         if [[ $ttest -eq 0 ]]; then
           t=06
         fi
	 t2=mpi128
      ;;
       -256 )
         if [[ $ttest -eq 0 ]]; then
           t=04
         fi
	 t2=mpi256
      ;;
       -r )
         r=1
      ;;
       -y )
         ask=0
      ;;
       -n[0-9]* )
         n=`echo $flag|sed 's/-n//'`
      ;;
       -* )
         echo ''
         echo 'Error: '$flag' is not a legal flag'
	 echo 'use qprep -h for help'
	 echo ''
	 exit
      ;;
       *.com )
       flag=`echo $flag|sed 's/\.com//'`
       filename=${filename}" "${flag}
      ;;
       * )
         echo ''
         echo 'Error: '$flag' needs to end in .com'
	 echo 'use qprep -h for help'
	 echo ''
	 exit
      ;;
  esac
done
 
# ....................................................................        
# Prepare the file         ...........................................
# ....................................................................        

if [[ $t -gt 24 && $t2 == "smp_normal" ]] ; then
  echo ""
  echo "Error:  You have requested more than 24 hours of walltime"
  echo "and the smp_normal queue.  Please request less than 24 hours"
  echo "of walltime to submit to the smp_normal queue"
  echo ""
  exit
fi

if [[ $n -gt 4 && $t2 == "smp_long" ]]  ; then
  echo ""
  echo "Error:  You have requested more than 4 cpus and the smp_long queue"
  echo "Please request 4 cpus or less to submit to the smp_long queue"
  echo ""
  exit
fi

if [[ $n -gt 16 && $t2 == "smp_normal" ]]  ; then
  echo ""
  echo "Error:  You have requested more than 16 cpus and the smp_normal queue"
  echo "Please request 16 cpus or less to submit to the smp_normal queue"
  echo ""
  exit
fi

if [[ $n -gt 16 && $t2 == "smp_normal" ]]  ; then
  echo ""
  echo "Error:  You have requested more than 16 cpus and the smp_normal queue"
  echo "Please request 16 cpus or less to submit to the smp_normal queue"
  echo ""
  exit
fi

if [[ $p == "g03" ]] ; then
  case "$t2" in 
     mpi* )
       echo ""
       echo "Error: Gaussian currently will not run in the mpi queues"
       echo "Please submit to the smp_normal or smp_long queue"
       echo ""
       exit
      ;;
  esac
fi

let "memtest=($mg)/($n*125000000)"
if [[ $memtest -gt 2 ]]; then
  echo ""
  echo "Warning: you should only specify up to 2 GB per processor."
  echo ""
  echo -n 'Do you want to continue? (y or n) '

  read cont

  if [[ $cont == "n" || $cont == "no" || $cont == "N" || $cont == "NO" || $cont == "No" ]]; then
   exit
  fi
fi

for data in $filename ; do
  if [[ $p == "g03" && ! -e ${data}.com ]] ; then
    echo "***************************************************"
    echo " Error: The input file "${data}".com does not exist  "
    echo "***************************************************"
  else
    echo '#@ shell		  = /bin/bash' > $data.job
    echo '#@ comment		  = '$data >> $data.job
    echo '#@ job_name		  = '$data >> $data.job
    echo '#@ error		  = $(job_name).job.e$(jobid)' >> $data.job
    echo '#@ output		  = $(job_name).job.o$(jobid)' >> $data.job
    echo '#@ wall_clock_limit	  = '$t':00:00' >> $data.job
#    if [[ $n -eq 1 ]] ; then
      echo '#@ job_type 	    = serial' >> $data.job
#    else
#      echo '#@ job_type 	    = parallel' >> $data.job
#    fi
    echo '#@ resources  	  = ConsumableCpus('$n') ConsumableMemory('$m')' >> $data.job
    echo '#@ node_usage 	  = shared' >> $data.job
    echo '#@ notification	  = complete' >> $data.job
    echo '#@ queue' >> $data.job
    echo '#' >> $data.job
    echo '' >> $data.job
    echo '# in case the job runs out of time, grab the job info' >> $data.job
    echo 'trap "echo -n End Date: ;date;echo accounting;ls -al /work/$LOADL_STEP_ID;llq -lx $LOADL_STEP_ID;llq -w $LOADL_STEP_ID" 0 1 2 3 15' >> $data.job
    echo '' >> $data.job
    echo 'export OBJECT_MODE=64' >> $data.job
    echo '' >> $data.job
    echo 'export g03root=/usr/local/lms/g03_D02_new' >> $data.job
    echo '. $g03root/g03/bsd/g03.profile' >> $data.job
    echo '' >> $data.job
    echo 'export LIBPATH=/usr/local/xlf10.1/usr/lib' >> $data.job
    echo '' >> $data.job
    echo 'cd /work/$LOADL_STEP_ID' >> $data.job
    echo '' >> $data.job
    echo 'echo "-P-" '${n}' > Default.Route' >> $data.job
    echo 'echo "-M-" '${mg}' >> Default.Route' >> $data.job
    echo '' >> $data.job
    echo 'echo Environmental Settings' >> $data.job
    echo 'env' >> $data.job
    echo 'echo -n "Start Date: "' >> $data.job
    echo 'date' >> $data.job
    echo '' >> $data.job
    if [[ $r -eq 0 ]] ; then
      echo 'g03 < $LOADL_STEP_INITDIR/$LOADL_JOB_NAME.com > $LOADL_STEP_INITDIR/$LOADL_JOB_NAME.log' >> $data.job
    else
      echo 'g03 < $LOADL_STEP_INITDIR/$LOADL_JOB_NAME.com >> $LOADL_STEP_INITDIR/$LOADL_JOB_NAME.log' >> $data.job
    fi
    echo '' >> $data.job
    echo 'exit' >> $data.job

    echo '******************************************'
    if [[ $ask == 1 ]] ; then
      echo Look over the contents of your job file
      echo ''
      echo '<<<< Job file' ${data}.job '>>>>>'
      echo ''
      cat ${data}.job
      echo ''
      echo '<<<< end of Job file' ${data}.job '>>>>>'
      echo ''
      echo -n 'Do you want to submit this job? (y or n) '
  
      read submitit
    else
      submitit=y
    fi  
    if [[ $submitit == "y" || $submit == "yes" ]]; then
      llsubmit ${data}.job
      echo ''
      echo 'Your job has been submitted to the' ${t2} 'queue with a request for' ${t} 'hours of walltime,' ${m} 'memory and' ${n} 'processors'
      echo ''
    else
      echo 'Your job was NOT submitted to the' ${t2} 'queue with a request for' ${t} 'hours of walltime,' ${m} 'memory and' ${n} 'processors'
      echo 
      echo 'You may manually submit your job with the command llsubmit '$data'.job'
    fi
  
    echo ''
  fi
done

llq -f  %o %jn %jt %h %is %p %nh %id %dq %dd %c %st -u $LOGNAME

exit